GeneBe

10-45374099-TGCGGGGGCGGGGGCGGGGGCGGGG-TGCGGGGGCGGGGGCGGGG

Variant names:

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_000698.5(ALOX5):​c.-180_-175delGCGGGG variant causes a upstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 821,412 control chromosomes in the GnomAD database, including 6,828 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.16 ( 2090 hom., cov: 22)
Exomes 𝑓: 0.089 ( 4738 hom. )

Consequence

ALOX5
NM_000698.5 upstream_gene

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.450
Variant links:
Genes affected
ALOX5 (HGNC:435): (arachidonate 5-lipoxygenase) This gene encodes a member of the lipoxygenase gene family and plays a dual role in the synthesis of leukotrienes from arachidonic acid. The encoded protein, which is expressed specifically in bone marrow-derived cells, catalyzes the conversion of arachidonic acid to 5(S)-hydroperoxy-6-trans-8,11,14-cis-eicosatetraenoic acid, and further to the allylic epoxide 5(S)-trans-7,9-trans-11,14-cis-eicosatetrenoic acid (leukotriene A4). Leukotrienes are important mediators of a number of inflammatory and allergic conditions. Mutations in the promoter region of this gene lead to a diminished response to antileukotriene drugs used in the treatment of asthma and may also be associated with atherosclerosis and several cancers. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2012]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.206 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ALOX5NM_000698.5 linkc.-180_-175delGCGGGG upstream_gene_variant ENST00000374391.7 NP_000689.1 P09917-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ALOX5ENST00000374391.7 linkc.-180_-175delGCGGGG upstream_gene_variant 1 NM_000698.5 ENSP00000363512.2 P09917-1
ALOX5ENST00000542434.5 linkc.-180_-175delGCGGGG upstream_gene_variant 1 ENSP00000437634.1 P09917-2

Frequencies

GnomAD3 genomes
AF:
0.164
AC:
24617
AN:
149816
Hom.:
2086
Cov.:
22
show subpopulations
Gnomad AFR
AF:
0.160
Gnomad AMI
AF:
0.218
Gnomad AMR
AF:
0.132
Gnomad ASJ
AF:
0.165
Gnomad EAS
AF:
0.216
Gnomad SAS
AF:
0.197
Gnomad FIN
AF:
0.193
Gnomad MID
AF:
0.161
Gnomad NFE
AF:
0.163
Gnomad OTH
AF:
0.168
GnomAD4 exome
AF:
0.0894
AC:
60028
AN:
671494
Hom.:
4738
AF XY:
0.0926
AC XY:
30120
AN XY:
325374
show subpopulations
Gnomad4 AFR exome
AF:
0.110
Gnomad4 AMR exome
AF:
0.102
Gnomad4 ASJ exome
AF:
0.136
Gnomad4 EAS exome
AF:
0.197
Gnomad4 SAS exome
AF:
0.131
Gnomad4 FIN exome
AF:
0.197
Gnomad4 NFE exome
AF:
0.0776
Gnomad4 OTH exome
AF:
0.111
GnomAD4 genome
AF:
0.164
AC:
24644
AN:
149918
Hom.:
2090
Cov.:
22
AF XY:
0.166
AC XY:
12138
AN XY:
73096
show subpopulations
Gnomad4 AFR
AF:
0.160
Gnomad4 AMR
AF:
0.131
Gnomad4 ASJ
AF:
0.165
Gnomad4 EAS
AF:
0.217
Gnomad4 SAS
AF:
0.197
Gnomad4 FIN
AF:
0.193
Gnomad4 NFE
AF:
0.163
Gnomad4 OTH
AF:
0.167

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs59439148; hg19: chr10-45869547; API